Dear Dale, Thanks for your e-mail and I’m glad to hear from you. You may already have the background to understand different representations (e.g., cartoons, ribbons, etc.) so I apologize if some of the comments below are generic. I wrote this up for others interested in the project.
It’s important that Avogadro gains: - Support for tracking data needed to render a protein (or nucleic acid or sugar) - storing residue information, sequence/chain, etc. - How the rendering is done (e.g., how to use OpenGL or WebGL to draw a cartoon, ribbon, etc.) For example: - 3dmol.js - https://github.com/3dmol/3Dmol.js/blob/master/3Dmol/glcartoon.js - ngl - https://github.com/arose/ngl/blob/master/src/representation/cartoon-representation.js (I can't find the PyMol cartoon code, but it'd be worth finding that.) - Avogadro1 - https://github.com/cryos/avogadro/blob/master/libavogadro/src/engines/cartoonmeshgenerator.cpp There are also academic papers on protein rendering that would be useful to read: - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672931/ - https://academic.oup.com/nar/article/43/W1/W576/2467902 - http://doi.wiley.com/10.1111/cgf.13072 - http://ieeexplore.ieee.org/document/1372203/ - http://ieeexplore.ieee.org/document/1320224/ Consider also, how can you use symmetry to improve rendering speed? Should the implementation use GPU, CPU or CPU/GPU hybrid approaches? If you can’t access any of the articles, please let me know. Hope that helps - let us know if you have further questions when drafting a proposal! -Geoff > On Mar 22, 2018, at 1:28 PM, Erikson, Dale J <dj...@pitt.edu> wrote: > > Dear Dr. Hutchison, > > My name is Dale and I am an undergraduate student at Pitt interested in > Google Summer of Code. In searching for a project, I wanted to find something > that combined my passion for computer science and biochemistry. To my > delight, I came across the idea to implement biological data visualization in > Avogadro 2. > > Through this email, I wanted to introduce myself and express my interest in > developing this feature. I think it would be a wonderful experience to work > with such a strong and influential presence in computational chemistry. > Additionally, I wanted to ask if you had any extra information you would like > to see in a proposal other than what is currently listed. > > I look forward to submitting my application. > > Have a great day, > > Dale Erikson > Dietrich School of Arts & Sciences, University of Pittsburgh > Computer Science | Molecular Biology > 908-627-6741 | dj...@pitt.edu ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
